Enzymatic Reaction Mechanisms 1st Edition by Perry Frey, Adrian Hegeman 0195122585 9780195122589

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ISBN 10: 0195122585
ISBN 13: 9780195122589
Author: Perry A. Frey, Adrian D. Hegeman

Books dealing with the mechanisms of enzymatic reactions were written a generation ago. They included volumes entitled Bioorganic Mechanisms, I and II by T.C. Bruice and S.J. Benkovic, published in 1965, the volume entitled Catalysis in Chemistry and Enzymology by W.P. Jencks in 1969, and the volume entitled Enzymatic Reaction Mechanisms by C.T. Walsh in 1979. The Walsh book was based on the course taught by W.P. Jencks and R.H. Abeles at Brandeis University in the 1960’s and 1970’s. By the late 1970’s, much more could be included about the structures of enzymes and the kinetics and mechanisms of enzymatic reactions themselves, and less emphasis was placed on chemical models. Walshs book was widely used in courses on enzymatic mechanisms for many years. Much has happened in the field of mechanistic enzymology in the past 15 to 20 years. Walshs book is both out-of-date and out-of-focus in todays world of enzymatic mechanisms. There is no longer a single volume or a small collection of volumes to which students can be directed to obtain a clear understanding of the state of knowledge regarding the chemicals mechanisms by which enzymes catalyze biological reactions. There is no single volume to which medicinal chemists and biotechnologists can refer on the subject of enzymatic mechanisms. Practitioners in the field have recognized a need for a new book on enzymatic mechanisms for more than ten years, and several, including Walsh, have considered undertaking to modernize Walshs book. However, these good intentions have been abandoned for one reason or another. The great size of the knowledge base in mechanistic enzymology has been a deterrent. It seems too large a subject for a single author, and it is difficult for several authors to coordinate their work to mutual satisfaction. This text by Perry A. Frey and Adrian D. Hegeman accomplishes this feat, producing the long-awaited replacement for Walshs classic text.

Enzymatic Reaction Mechanisms 1st Table of contents

Chapter 1. Enzymes and Catalytic Mechanisms
Catalysis and the Active Site
Rate Enhancement in Enzymatic Catalysis
Conformational Mobility in Catalysis
Substrate-Induced Conformational Changes
Catalysis of Multistep Reactions
Structural Mobility in Enzymes
Acid-Base Catalysis
Acids and Bases
Acidand Base-Catalyzed Reactions
Nucleophilic Catalysis
Electrophilic Catalysis
Catalysis of Enolization
Imine Formation by Lysine
Catalysis by Metal Ions
Hydrogen Bonding
Strong and Weak Hydrogen Bonds
Hydrogen Bonding in Catalysis
Binding Energy in Catalysis
Binding and Activation Energy
The Active Site as an Entropy Trap
Dissecting the Binding Effect in Enzymatic Action
Stabilization of the Transition State
Binding the Near Attack Conformation
Destabilization of Ground States
Rate Enhancement through Binding of Remote Groups
Characterization of Active Sites
Competitive Inhibitors: Analogs of Substrates
Group-Selective Chemical Modification
Site-Directed Mutagenesis
Affinity Labeling
Why Are Enzymes Large Molecules?
Sizes of Enzymatic Binding Domains
Catalytic Antibodies
Chapter 2. Kinetics of Enzymatic Reactions
Steady-State Kinetics
One-Substrate Reactions
Two-Substrate Reactions
Three-Substrate Reactions
Isotope Effects
Classes of Isotope Effects
Measurement of Isotope Effects
Transient-Phase Kinetics
Reaction Characteristics
Transient Methods
pH-Rate Profiles
Profile Interpretation
Measurements of pH-Rate Profiles
Allosteric Regulation
Theory
Binding Equations for Cooperative Systems
Aspartate Transcarbamoylase
Chapter 3. Coenzymes I: Organic Coenzymes
Nicotinamide Coenzymes
Structures and Functions of Nicotinamide Coenzymes
Stereospecificity of Hydride Transfer
NAD+ as a Coenzyme
Thiamine Pyrophosphate
Structure
Reaction Mechanism
α-Lipoamide
Pyridoxal-5P-Phosphate
Enzymatic Reactions Facilitated by Pyridoxal-5>-Phosphate
Pyridoxal-5–Phosphate–Stabilized Amino Acid Carbanions
Mechanisms of Pyridoxal-5l-Phosphate–Dependent Reactions
Flavin Coenzymes
Structures of Flavin Coenzymes
Mechanisms of Flavin Catalysis
Biotin
Structure and Role as a Carboxyl Carrier
Chemistry of Biotin and N1-Carboxybiotin
Mechanism of Biotin-Dependent Carboxylation
Phosphopantetheine Coenzymes
Structures of Phosphopantetheine Coenzymes
Mechanism of Phosphopantetheine Action
Folate Compounds
Folate Compounds of One-Carbon Metabolism
Enzymes in Tetrahydrofolate Metabolism
Biological Importance of Folate
Amino Acid–Based Coenzymes
Pyruvoyl Decarboxylases
Methylidene Imidazolinone–Dependent Deaminases
Quinoproteins
Chapter 4. Coenzymes II: Metallic Coenzymes
Vitamin B12 Coenzymes
Chemistry of B12 Coenzymes
Adenosylcobalamin-Dependent Enzymes
Methylcobalamin-Dependent Enzymes
Heme Coenzymes
Chemistry of Oxygen and Heme
Heme Enzymes
Oxygen Binding and Electron Transfer
Mononuclear Nonheme Iron
Monooxygenases
Dioxygenases
Oxo-Fe2 Complexes
Structures
Reactions of Di-iron Enzymes
Metallopterin Enzymes
Molybdopterin and Tungstopterin
Iron-Sulfur Centers
Structures
Catalytic Functions
S-Adenosylmethionine and Iron-Sulfur Centers
Catalytic Action of S-Adenosylmethionine and [4Fe–4S] Centers
Stoichiometric Reactions of S-Adenosylmethionine and [4Fe–4S] Centers
Divalent Metal Ions
Electrostatic Activation of Coordinated Water
Electrostatic Activation of Enolization
Copper as a Cofactor
Copper Proteins
Other Copper Enzymes
Nickel Coenzymes
Nickel in Methanogenesis
Other Nickel Coenzymes
Long-Range Electron Transfer
Biological Electron Transfer
Marcus Theory
Chapter 5. Enzyme Inhibition
Two-Substrate Analogs
Inhibition and Binding
PALA and Aspartate Transcarbamylase
Suicide Inactivation
Thymidylate Synthase
β-Hydroxydecanoyl Thioester Dehydratase
γAminobutyrate Aminotransferase
Kinetics of Slow-Binding and Tight-Binding Inhibition
Slow Binding
Tight Binding
Slow-Binding Inhibition
Dihydrofolate Reductase
Prostaglandin H Synthase
Tight-Binding Inhibition
HMG-CoA Reductase
Alanine Racemase
5-Enolpyruvoylshikimate-3-Phosphate Synthase
Acetylcholinesterase
Chapter 6. Acyl Group Transfer: Proteases and Esterases
Chemistry of Acyl Transfer
Serine Proteases
Chymotrypsin
Subtilisin
Cysteine Proteases
Papain
Caspases
Aspartic Proteases
Molecular Properties
Mechanism of Action
Metalloproteases
Carboxypeptidase A
Thermolysin
Esterases
Structure and Function
Phospholipase A2
Chapter 7. Isomerization
Aldose and Ketose Isomerases
Chemistry
Phosphoglucose Isomerase
Triosephosphate Isomerase
Xylose Isomerase
Phosphomutases
αPhosphoglucomutase
βPhosphoglucomutase
Phosphoglycerate Mutases
Racemases and Epimerases
Proline Racemase
Glutamate Racemase
Mandelate Racemase
UDP-Galactose 4-Epimerase
Ribulose-5-P 4-Epimerase
UDP-N-Acetylglucosamine-2-Epimerase
Chorismate Mutase
Δ5-3-Ketosteroid Isomerase
Radical Isomerizations
Glutamate Mutase
Methylmalonyl CoA Mutase
Lysine 2,3-Aminomutase
Newer Isomerases
UDP-Galactopyranose Mutase
Pseudouridine Synthase
Chapter 8. Decarboxylation and Carboxylation
Chemistry of Decarboxylation and Carboxylation
Decarboxylases
Pyruvate Decarboxylase
Amino Acid Decarboxylases
Acetoacetate Decarboxylase
Mevalonate Pyrophosphate Decarboxylase
Radical-Based Decarboxylases
Orotidine Monophosphate Decarboxylase
Carboxylases
Ribulose-1,5-Bisphosphate Carboxylase
Phosphoenolpyruvate Carboxylase
Vitamin K–Dependent Carboxylase
Chapter 9. Addition and Elimination
α,β-Elimination/Addition Reactions
Cofactor-Independent α,β-Elimination/Addition Reactions
Cofactor-Dependent α,β-Elimination/Addition Reactions
α,β-Elimination/Addition Reactions
Methylidene Imidazolone–Dependent Elimination and Addition
Carbonic Anhydrase
Isomerization and Elimination
Catalytic Process
Coenzyme B12–Dependent Elimination
Chapter 10. Phosphotransfer and Nucleotidyltransfer
Chemistry of Phosphoryl Group Transfer
Phosphomonoesters
Phosphodiesters
Phosphotriesters
Five-Member Ring Phosphoesters
Enzymatic Phosphoryl Group Transfer
Single and Double Displacements
Phosphotransferases
Protein Phosphorylation: Protein Kinase A
Phosphomonoesterases
Enzymatic Nucleotidyl Group Transfer
Nucleotidyltransferases
Phosphodiesterases
Chapter 11. ATP-Dependent Synthetases and Ligases
Ligation and the Energy of ATP
Activation by Phosphorylation
Glutamine Synthetase
Carbamoyl Phosphate Synthetase
Activation by Adenylylation
DNA Ligase
Aminoacyl-tRNA Synthetases
Ubiquitin
Chapter 12. Glycosyl Group Transferases
Chemical Mechanisms
Chemistry of Glycoside Hydrolysis
Enzymatic Glycosyl Transfer
Glycosyltransferases
Sucrose Phosphorylase
Glycogen Phosphorylase
Purine Nucleoside Phosphorylase
Glycosidases
Families and Structures
Lysozyme
T4 Lysozyme
Chapter 13. Nitrogen and Sulfur Transferases
Nitrogen Transfer
Aspartate Aminotransferase
Tyrosine 2,3-Aminomutase
Amidotransfer
Glutamine:PRPP Amidotransferase
Sulfur Transfer
Biotin Synthase
Lipoyl Synthase
Chapter 14. Carbon-Carbon Condensation and Cleavage
Chemistry
Enolization of Acetyl CoA
Acetyl CoA in Ester Condensations
Citrate Synthase
Thiolases
Carbanionic Mechanisms
Transaldolase
Transketolase
Serine Hydroxymethyltransferase
Carbocationic Mechanisms
Farnesyl Pyrophosphate Synthase
Squalene Synthase
Chapter 15. Alkyltransferases
Chemistry of Alkylation
Biological Alkylations
Alkylation Mechanisms
Enzymatic Alkylation
Protein Farnesyltransferase
Catechol O-Methyltransferase
S-Adenosylmethionine Synthetase
Methionine Synthases
Chapter 16. Oxidoreductases
Pyridine Nucleotide–Dependent Dehydrogenases
Alcohol Dehydrogenase
Lactate Dehydrogenase
Short-Chain Alcohol Dehydrogenases
Glyceraldehyde-3-P Dehydrogenase
Glutamate Dehydrogenase
Disulfide Oxidoreductases
Dihydrolipoyl Dehydrogenase
Ribonucleotide Reductases
Classes of Ribonucleotide Reductases
Structural Relationships of Ribonucleotide Reductases
Chapter 17. Oxidases and Oxygenases
Oxidases
D-Amino Acid Oxidase
Monoamine Oxidases
Isopenicillin-N Synthase
Urate Oxidase
Monooxygenases
Lactate Monooxygenase
Cytochrome P450 Monooxygenases
Iron-Methane Monooxygenase
α-Ketoglutarate–Dependent Oxygenases
Dopamine i-Monooxygenase
Copper-Methane Monooxygenase
Nitric Oxide Synthase
Dioxygenases
Intradiol Dioxygenases
Extradiol Dioxygenases
Chapter 18. Complex Enzymes
Multienzyme Complexes
α-Ketoacid Dehydrogenase Complexes
Pyruvate Dehydrogenase Complex
Fatty Acid Synthesis
Acetyl CoA Carboxylase
Fatty Acid Synthases
Modular Enzymes
Polyketide Synthases
Nonribosomal Polypeptide Synthetases
Ribosomal Protein Synthesis
RNA Polymerase
The Ribosome
Energy-Coupling Enzymes
Nitrogenase
Cytochrome c Oxidase
ATP Synthase
Myosin and Muscle Contraction

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